I'm tempted by boutique pups but the price was putting me off, then I came across Swineshead and Irongear pups. They're both uk based and swineshead do hand wound pups for the price of seymours, the irongear are, by what I've heard, as good as stock seymours for half the price. To put that in context the price I paid to put new pups in my Ibanez would have re-shoed all three of my electrics.
Now I love SD's but if I can get something more unique but with similar sound quality for the same cash or even less then I'm going to be tempted.
If I had the cash would I go for expensive boutique pups such as bareknukles? possibly, but I think I'd need a pretty nice axe to put them into, but I'd probably go for those over custom shop SD's but that mainly due to delivery practicalities, and the guys at bareknuckle are really helpful (and sell magnets.)